[Bill Salama]

I had the same problem and here is how I solved it. I have two computers each has CS6 and one of them the encoder won’t launch.
I copied the entire directory of C:Program FilesAdobeAdobe Media Encoder CS6
into a network drive, you can also user a USB drive.
Then renamed the directory on the computer that Encoder doesn’t work to something else
Then copied the good directory from the network drive, or USB drive, in the proper location.

Then started it and it worked.

BTY, I tried re-installing and the problem was still there.

Good luck!